I use the outliner to organize all my models. I don't use layers at all. Maybe I will get shot for saying that but that is just how I do it.
I find it easiest when going from cad to SU to copy my cad file to a new location and then do some major cleanup prior to insertion. I make sure everything is 2D, delete anything unwanted, change all the lines to one layer and one color. I make sure that all connections are made, no small gaps... usually I make polylines so I know if there is a gap. Then I import it to SU and go from there. That way I don't need to discard it later, I just use that data.
The script modelhead was talking about, I think, is makefaces. You select all your lines and run the script. It will fill in the faces without you having to draw lines to finish the face. You can get it here:
http://www.smustard.com/scripts/
modelhead, no worries mate.